diff --git a/README.md b/README.md index fee0a4a..2f24ba8 100644 --- a/README.md +++ b/README.md @@ -75,8 +75,8 @@ git clone https://github.com/hsmaan/Iniquitate.git - Run the Rscripts based on their order, through RStudio or the commandline ``` conda activate iniq_analysis - Rscript 05_Iniq_Control_Fig_2_Analysis_Plots.R - Rscript 06_Iniq_Control_Fig_2_Analysis_Stat_Tests.R + Rscript 01_Iniq_Control_Fig_2_Analysis_Plots.R + Rscript 02_Iniq_Control_Fig_2_Analysis_Stat_Tests.R ... ``` diff --git a/workflow/analysis/R/05_Iniq_Control_Fig_2_Analysis_Plots.R b/workflow/analysis/R/01_Iniq_Control_Fig_2_Analysis_Plots.R similarity index 96% rename from workflow/analysis/R/05_Iniq_Control_Fig_2_Analysis_Plots.R rename to workflow/analysis/R/01_Iniq_Control_Fig_2_Analysis_Plots.R index fa3ff0d..8704042 100644 --- a/workflow/analysis/R/05_Iniq_Control_Fig_2_Analysis_Plots.R +++ b/workflow/analysis/R/01_Iniq_Control_Fig_2_Analysis_Plots.R @@ -16,6 +16,14 @@ library(Cairo) # Helper functions `%ni%` <- Negate(`%in%`) +# Create output directories if not made already +if (!dir.exists("outs/control/figures/")) { + dir.create("outs/control/figures/", recursive = TRUE) +} +if (!dir.exists("outs/control/results/")) { + dir.create("outs/control/results/", recursive = TRUE) +} + # Change to results dir for control data setwd("../../../results/control/") @@ -182,7 +190,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes.pdf", width = 6, height = 6 ) @@ -195,7 +203,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch.pdf", width = 6, height = 6 ) @@ -214,7 +222,7 @@ DimPlot(pbmc_combined_cd14_ablate, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes_cd14_ablate.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes_cd14_ablate.pdf", width = 6, height = 6 ) @@ -227,7 +235,7 @@ DimPlot(pbmc_combined_cd14_ablate, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch_cd14_ablate.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch_cd14_ablate.pdf", width = 6, height = 6 ) @@ -252,7 +260,7 @@ DimPlot(pbmc_combined_cd14_ds, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes_cd14_10_pct_ds.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes_cd14_10_pct_ds.pdf", width = 6, height = 6 ) @@ -265,7 +273,7 @@ DimPlot(pbmc_combined_cd14_ds, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch_cd14_10_pct_ds.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch_cd14_10_pct_ds.pdf", width = 6, height = 6 ) @@ -407,7 +415,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_celltype_ari_ds_effects_heatmap.pdf", + "outs/control/figures/01_celltype_ari_ds_effects_heatmap.pdf", width = 8, height = 6 ) @@ -515,7 +523,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_batch_ari_ds_effects_heatmap.pdf", + "outs/control/figures/01_batch_ari_ds_effects_heatmap.pdf", width = 8, height = 6 ) @@ -617,7 +625,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_allmethod_knn_f1_score.pdf", + "outs/control/figures/01_pbmc_ds_ablate_allmethod_knn_f1_score.pdf", width = 12, height = 14, device = cairo_pdf @@ -710,7 +718,7 @@ ggscatter(median_imba_knn_cluster_results_cari, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_f1_score_celltype_ari_corr.pdf", + "outs/control/figures/01_pbmc_ds_ablate_f1_score_celltype_ari_corr.pdf", width = 14, height = 8, device = cairo_pdf @@ -758,7 +766,7 @@ ggscatter(median_imba_knn_cluster_results_bari, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_f1_score_batch_ari_corr.pdf", + "outs/control/figures/01_pbmc_ds_ablate_f1_score_batch_ari_corr.pdf", width = 14, height = 8, device = cairo_pdf @@ -921,7 +929,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_hierarchical_combined_celltypes.pdf", + "outs/control/figures/01_pbmc_balanced_hierarchical_combined_celltypes.pdf", width = 6, height = 6 ) @@ -934,7 +942,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_hierarchical_combined_batch.pdf", + "outs/control/figures/01_pbmc_balanced_hierarchical_combined_batch.pdf", width = 6, height = 6 ) @@ -955,7 +963,7 @@ DimPlot(pbmc_combined_nkt_ablate, reduction = "umap", group.by = "celltype") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_celltypes_nkt_ablate.pdf" + "01_pbmc_balanced_hierarchical_combined_celltypes_nkt_ablate.pdf" ), width = 6, height = 6 @@ -971,7 +979,7 @@ DimPlot(pbmc_combined_nkt_ablate, reduction = "umap", group.by = "batch") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_batch_nkt_ablate.pdf" + "01_pbmc_balanced_hierarchical_combined_batch_nkt_ablate.pdf" ), width = 6, height = 6 @@ -999,7 +1007,7 @@ DimPlot(pbmc_combined_nkt_ds, reduction = "umap", group.by = "celltype") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_celltypes_nkt_10_pct_ds.pdf" + "01_pbmc_balanced_hierarchical_combined_celltypes_nkt_10_pct_ds.pdf" ), width = 6, height = 6 @@ -1015,7 +1023,7 @@ DimPlot(pbmc_combined_nkt_ds, reduction = "umap", group.by = "batch") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_combined_batch_nkt_10_pct_ds.pdf" + "01_pbmc_balanced_combined_batch_nkt_10_pct_ds.pdf" ), width = 6, height = 6 @@ -1094,7 +1102,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score.pdf", + "outs/control/figures/01_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score.pdf", width = 8, height = 14, device = cairo_pdf @@ -1286,7 +1294,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes.pdf", width = 6, height = 6 ) @@ -1299,7 +1307,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch.pdf", width = 6, height = 6 ) @@ -1318,7 +1326,7 @@ DimPlot(pbmc_combined_cd14_ablate, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes_cd14_ablate.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes_cd14_ablate.pdf", width = 6, height = 6 ) @@ -1331,7 +1339,7 @@ DimPlot(pbmc_combined_cd14_ablate, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch_cd14_ablate.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch_cd14_ablate.pdf", width = 6, height = 6 ) @@ -1356,7 +1364,7 @@ DimPlot(pbmc_combined_cd14_ds, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_celltypes_cd14_10_pct_ds.pdf", + "outs/control/figures/01_pbmc_balanced_combined_celltypes_cd14_10_pct_ds.pdf", width = 6, height = 6 ) @@ -1369,7 +1377,7 @@ DimPlot(pbmc_combined_cd14_ds, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_combined_batch_cd14_10_pct_ds.pdf", + "outs/control/figures/01_pbmc_balanced_combined_batch_cd14_10_pct_ds.pdf", width = 6, height = 6 ) @@ -1511,7 +1519,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_celltype_ari_ds_effects_heatmap_no_liger.pdf", + "outs/control/figures/01_celltype_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 6 ) @@ -1622,7 +1630,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_celltype_balanced_ari_ds_effects_heatmap_no_liger.pdf", + "outs/control/figures/01_celltype_balanced_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 6 ) @@ -1730,7 +1738,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_batch_ari_ds_effects_heatmap_no_liger.pdf", + "outs/control/figures/01_batch_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 6 ) @@ -1867,7 +1875,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_celltype_ari_unscaled_ds_effects_heatmap_no_liger.pdf", + "outs/control/figures/01_celltype_ari_unscaled_ds_effects_heatmap_no_liger.pdf", width = 8, height = 6 ) @@ -1965,7 +1973,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/05_batch_ari_unscaled_ds_effects_heatmap_no_liger.pdf", + "outs/control/figures/01_batch_ari_unscaled_ds_effects_heatmap_no_liger.pdf", width = 8, height = 6 ) @@ -2066,7 +2074,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_allmethod_knn_f1_score_no_liger.pdf", + "outs/control/figures/01_pbmc_ds_ablate_allmethod_knn_f1_score_no_liger.pdf", width = 12, height = 14, device = cairo_pdf @@ -2106,7 +2114,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_allmethod_knn_f1_score_no_liger_0_1_y.pdf", + "outs/control/figures/01_pbmc_ds_ablate_allmethod_knn_f1_score_no_liger_0_1_y.pdf", width = 12, height = 14, device = cairo_pdf @@ -2139,7 +2147,7 @@ colnames(imba_knn_merged_celltype_medians_stdev) <- c( ) fwrite( imba_knn_merged_celltype_medians_stdev, - "outs/control/results/05_baseline_pbmc_f1_score_stdevs_per_celltype.tsv", + "outs/control/results/01_baseline_pbmc_f1_score_stdevs_per_celltype.tsv", sep = "\t", row.names = FALSE, col.names = TRUE @@ -2250,7 +2258,7 @@ ggscatter(median_imba_knn_cluster_results_cari, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_f1_score_celltype_ari_corr_no_liger.pdf", + "outs/control/figures/01_pbmc_ds_ablate_f1_score_celltype_ari_corr_no_liger.pdf", width = 14, height = 8, device = cairo_pdf @@ -2317,7 +2325,7 @@ ggscatter(median_imba_knn_cluster_results_bari, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/05_pbmc_ds_ablate_f1_score_batch_ari_corr_no_liger.pdf", + "outs/control/figures/01_pbmc_ds_ablate_f1_score_batch_ari_corr_no_liger.pdf", width = 14, height = 8, device = cairo_pdf @@ -2490,7 +2498,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_hierarchical_combined_celltypes.pdf", + "outs/control/figures/01_pbmc_balanced_hierarchical_combined_celltypes.pdf", width = 6, height = 6 ) @@ -2503,7 +2511,7 @@ DimPlot(pbmc_combined, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control/figures/05_pbmc_balanced_hierarchical_combined_batch.pdf", + "outs/control/figures/01_pbmc_balanced_hierarchical_combined_batch.pdf", width = 6, height = 6 ) @@ -2524,7 +2532,7 @@ DimPlot(pbmc_combined_nkt_ablate, reduction = "umap", group.by = "celltype") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_celltypes_nkt_ablate.pdf" + "01_pbmc_balanced_hierarchical_combined_celltypes_nkt_ablate.pdf" ), width = 6, height = 6 @@ -2540,7 +2548,7 @@ DimPlot(pbmc_combined_nkt_ablate, reduction = "umap", group.by = "batch") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_batch_nkt_ablate.pdf" + "01_pbmc_balanced_hierarchical_combined_batch_nkt_ablate.pdf" ), width = 6, height = 6 @@ -2568,7 +2576,7 @@ DimPlot(pbmc_combined_nkt_ds, reduction = "umap", group.by = "celltype") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_hierarchical_combined_celltypes_nkt_10_pct_ds.pdf" + "01_pbmc_balanced_hierarchical_combined_celltypes_nkt_10_pct_ds.pdf" ), width = 6, height = 6 @@ -2584,7 +2592,7 @@ DimPlot(pbmc_combined_nkt_ds, reduction = "umap", group.by = "batch") + ggsave( paste0( "outs/control/figures/", - "05_pbmc_balanced_combined_batch_nkt_10_pct_ds.pdf" + "01_pbmc_balanced_combined_batch_nkt_10_pct_ds.pdf" ), width = 6, height = 6 @@ -2663,7 +2671,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score_no_liger_ylim_0.5_1.pdf", + "outs/control/figures/01_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score_no_liger_ylim_0.5_1.pdf", width = 8, height = 14, device = cairo_pdf @@ -2703,7 +2711,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/05_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score_no_liger_y_0_1.pdf", + "outs/control/figures/01_pbmc_hierarchical_ds_ablate_allmethod_knn_f1_score_no_liger_y_0_1.pdf", width = 8, height = 14, device = cairo_pdf diff --git a/workflow/analysis/R/06_Iniq_Control_Fig_2_Analysis_Stat_Tests.R b/workflow/analysis/R/02_Iniq_Control_Fig_2_Analysis_Stat_Tests.R similarity index 98% rename from workflow/analysis/R/06_Iniq_Control_Fig_2_Analysis_Stat_Tests.R rename to workflow/analysis/R/02_Iniq_Control_Fig_2_Analysis_Stat_Tests.R index 0418796..e1c1553 100644 --- a/workflow/analysis/R/06_Iniq_Control_Fig_2_Analysis_Stat_Tests.R +++ b/workflow/analysis/R/02_Iniq_Control_Fig_2_Analysis_Stat_Tests.R @@ -256,7 +256,7 @@ global_metric_results_indi_pooled <- rbind( ) fwrite( global_metric_results_indi_pooled, - "outs/control/results/06_pbmc_base_global_metric_wilcoxon_tests.tsv", + "outs/control/results/02_pbmc_base_global_metric_wilcoxon_tests.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -349,7 +349,7 @@ metric_aov_results_concat$`FDR_q` <- p.adjust( ) fwrite( metric_aov_results_concat, - "outs/control/results/06_pbmc_base_metric_aov_results_types_ct_method_ctrl.tsv", + "outs/control/results/02_pbmc_base_metric_aov_results_types_ct_method_ctrl.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -481,7 +481,7 @@ global_celltype_knn_results_type_and_pooled <- rbind( ) fwrite( global_celltype_knn_results_type_and_pooled, - "outs/control/results/06_pbmc_base_knn_cell_ds_cell_test_wilcoxon_tests.tsv", + "outs/control/results/02_pbmc_base_knn_cell_ds_cell_test_wilcoxon_tests.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -545,7 +545,7 @@ fwrite( knn_aov_results, paste0( "outs/control/results/", - "06_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype.tsv" + "02_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype.tsv" ), sep = "\t", quote = FALSE, @@ -743,7 +743,7 @@ fwrite( global_celltype_knn_results_type_and_pooled, paste0( "outs/control/results/", - "06_pbmc_hierarchical_knn_cell_ds_cell_test_wilcoxon_tests.tsv" + "02_pbmc_hierarchical_knn_cell_ds_cell_test_wilcoxon_tests.tsv" ), sep = "\t", quote = FALSE, @@ -778,7 +778,7 @@ fwrite( knn_aov_results, paste0( "outs/control/results/", - "06_pbmc_hierarchical_knn_cell_ds_cell_aov_results_ctrl_method_ds_celltype.tsv" + "02_pbmc_hierarchical_knn_cell_ds_cell_aov_results_ctrl_method_ds_celltype.tsv" ), sep = "\t", quote = FALSE, @@ -1055,7 +1055,7 @@ global_metric_results_indi_pooled <- rbind( ) fwrite( global_metric_results_indi_pooled, - "outs/control/results/06_pbmc_base_global_metric_wilcoxon_tests_no_liger.tsv", + "outs/control/results/02_pbmc_base_global_metric_wilcoxon_tests_no_liger.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -1148,7 +1148,7 @@ metric_aov_results_concat$`FDR_q` <- p.adjust( ) fwrite( metric_aov_results_concat, - "outs/control/results/06_pbmc_base_metric_aov_results_types_ct_method_ctrl_no_liger.tsv", + "outs/control/results/02_pbmc_base_metric_aov_results_types_ct_method_ctrl_no_liger.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -1280,7 +1280,7 @@ global_celltype_knn_results_type_and_pooled <- rbind( ) fwrite( global_celltype_knn_results_type_and_pooled, - "outs/control/results/06_pbmc_base_knn_cell_ds_cell_test_wilcoxon_tests_no_liger.tsv", + "outs/control/results/02_pbmc_base_knn_cell_ds_cell_test_wilcoxon_tests_no_liger.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -1344,7 +1344,7 @@ fwrite( knn_aov_results, paste0( "outs/control/results/", - "06_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype_no_liger.tsv" + "02_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -1543,7 +1543,7 @@ fwrite( global_celltype_knn_results_type_and_pooled, paste0( "outs/control/results/", - "06_pbmc_hierarchical_knn_cell_ds_cell_test_wilcoxon_tests_no_liger.tsv" + "02_pbmc_hierarchical_knn_cell_ds_cell_test_wilcoxon_tests_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -1578,7 +1578,7 @@ fwrite( knn_aov_results, paste0( "outs/control/results/", - "06_pbmc_hierarchical_knn_cell_ds_cell_aov_results_ctrl_method_ds_celltype_no_liger.tsv" + "02_pbmc_hierarchical_knn_cell_ds_cell_aov_results_ctrl_method_ds_celltype_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -1594,7 +1594,7 @@ knn_aov_results_hierarchical <- knn_aov_results knn_aov_results_baseline <- fread( paste0( "outs/control/results/", - "06_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype_no_liger.tsv" + "02_pbmc_base_knn_cell_ds_cell_aov_results_ctrl_method_celltype_no_liger.tsv" ) ) @@ -1670,7 +1670,7 @@ ggplot(data = knn_aov_comp_df_melted, aes(Covariates, value)) + ggsave( paste0( "outs/control/figures/", - "06_pbmc_base_vs_hierarchical_knn_aov_results_comp_no_liger.pdf" + "02_pbmc_base_vs_hierarchical_knn_aov_results_comp_no_liger.pdf" ), width = 12, height = 8, diff --git a/workflow/analysis/R/07_Iniq_Control_Fig_3_Analysis_Plots.R b/workflow/analysis/R/03_Iniq_Control_Fig_3_Analysis_Plots.R similarity index 97% rename from workflow/analysis/R/07_Iniq_Control_Fig_3_Analysis_Plots.R rename to workflow/analysis/R/03_Iniq_Control_Fig_3_Analysis_Plots.R index 44404c7..8c063d7 100644 --- a/workflow/analysis/R/07_Iniq_Control_Fig_3_Analysis_Plots.R +++ b/workflow/analysis/R/03_Iniq_Control_Fig_3_Analysis_Plots.R @@ -224,7 +224,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_allmethod_cluster_number.pdf", + "outs/control/figures/03_pbmc_ds_ablate_allmethod_cluster_number.pdf", width = 14, height = 8, device = cairo_pdf @@ -262,7 +262,7 @@ ggscatter(imba_clus_merged, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_clus_num_celltype_ari_corr.pdf", + "outs/control/figures/03_pbmc_ds_ablate_clus_num_celltype_ari_corr.pdf", width = 14, height = 8, device = cairo_pdf @@ -297,7 +297,7 @@ ggscatter(imba_clus_merged, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_clus_num_batch_ari_corr.pdf", + "outs/control/figures/03_pbmc_ds_ablate_clus_num_batch_ari_corr.pdf", width = 14, height = 8, device = cairo_pdf @@ -381,7 +381,7 @@ ggplot(data = imba_dge_merged, aes( theme(legend.position = "None") ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "marker_gene_max_ranks.pdf" ), width = 14, @@ -436,7 +436,7 @@ ggplot(data = imba_dge_merged, aes( theme(legend.position = "None") ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "marker_gene_max_ranks_per_method.pdf" ), width = 14, @@ -491,7 +491,7 @@ lapply(methods, function(x) { dge_method_plt(imba_dge_merged, x) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", x, "_dge_rankings.pdf" ), @@ -648,7 +648,7 @@ ht4 <- Heatmap( # Plot and save all of the heatmaps together marker_pert_hm <- ht1 + ht2 + ht3 + ht4 CairoPDF( - "outs/control/figures/07_marker_gene_pert_pbmc_control_heatmap.pdf", + "outs/control/figures/03_marker_gene_pert_pbmc_control_heatmap.pdf", width = 14, height = 6 ) @@ -712,7 +712,7 @@ ht3 <- Heatmap( ) marker_per_hm_no_celltype <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/07_marker_gene_pert_pbmc_control_heatmap_no_ctype.pdf", + "outs/control/figures/03_marker_gene_pert_pbmc_control_heatmap_no_ctype.pdf", width = 14, height = 6 ) @@ -770,7 +770,7 @@ ggplot(imba_dge_merged_top_10_var_genes, aes(x = Gene, y = `Max rank`)) + theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_dge_rankings_top_10_var_genes.pdf" + "outs/control/figures/03_pbmc_ds_ablate_dge_rankings_top_10_var_genes.pdf" ), width = 14, height = 8, @@ -839,7 +839,7 @@ lapply(methods, function(x) { dge_stdev_method_plt(gene_rank_variance_grouped, x) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", x, "_dge_rankings_method_type_stdev.pdf" ), @@ -898,7 +898,7 @@ ggplot( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_dge_rankings_method_type_stdev_top_10.pdf" ), width = 14, @@ -961,7 +961,7 @@ ggplot( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_dge_rankings_type_stdev.pdf" ), width = 14, @@ -1031,7 +1031,7 @@ top_10_var_marker_genes_sankey <- sankeyNetwork( saveNetwork( top_10_var_marker_genes_sankey, file = paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_top_var_dges_with_assoc_celltypes.html" ), selfcontained = TRUE @@ -1174,7 +1174,7 @@ ggplot( ) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_only_", + "outs/control/figures/03_pbmc_ds_only_", "_dge_rankings_celltype_marker_celltype_ds_compare.pdf" ), width = 14, @@ -1235,7 +1235,7 @@ ggplot( ) ggsave( paste0( - "outs/control/figures/07_pbmc_ablated_only_", + "outs/control/figures/03_pbmc_ablated_only_", "_dge_rankings_celltype_marker_celltype_ablated_compare.pdf" ), width = 14, @@ -1387,7 +1387,7 @@ ggplot(data = imba_anno_merged_score_format_l1, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_ds.pdf" + "03_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_ds.pdf" ), width = 16, height = 7, @@ -1429,7 +1429,7 @@ ggplot(data = imba_anno_merged_score_format_l2, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_ds.pdf" + "03_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_ds.pdf" ), width = 16, height = 7, @@ -1486,7 +1486,7 @@ ggplot(data = imba_anno_merged_score_format_l1_sd, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_sdev.pdf" + "03_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_sdev.pdf" ), width = 7, height = 5, @@ -1530,7 +1530,7 @@ ggplot(data = imba_anno_merged_score_format_l2_sd, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_sdev.pdf" + "03_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_sdev.pdf" ), width = 7, height = 5, @@ -1628,7 +1628,7 @@ ggplot(data = imba_anno_merged_all_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_t_cell_preds_barplot.pdf" + "03_pbmc_ds_ablate_l1_annotation_t_cell_preds_barplot.pdf" ), width = 10, height = 7, @@ -1660,7 +1660,7 @@ ggplot(data = imba_anno_merged_all_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_t_cell_preds_barplot.pdf" + "03_pbmc_ds_ablate_l2_annotation_t_cell_preds_barplot.pdf" ), width = 10, height = 7, @@ -1704,7 +1704,7 @@ ggplot(data = imba_anno_merged_all_cd4_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_cd4t_cell_preds", + "03_pbmc_ds_ablate_l1_annotation_cd4t_cell_preds", "_celltype_ds_specific_barplots.pdf" ), width = 12, @@ -1737,7 +1737,7 @@ ggplot(data = imba_anno_merged_all_cd4_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_cd4t_cell_preds", + "03_pbmc_ds_ablate_l2_annotation_cd4t_cell_preds", "_celltype_ds_specific_barplots.pdf" ), width = 12, @@ -1770,7 +1770,7 @@ ggplot(data = imba_anno_merged_all_cd8_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_cd8t_cell_preds", + "03_pbmc_ds_ablate_l1_annotation_cd8t_cell_preds", "_celltype_ds_specific_barplots.pdf" ), width = 12, @@ -1803,7 +1803,7 @@ ggplot(data = imba_anno_merged_all_cd8_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_cd8t_cell_preds", + "03_pbmc_ds_ablate_l2_annotation_cd8t_cell_preds", "_celltype_ds_specific_barplots.pdf" ), width = 12, @@ -1857,7 +1857,7 @@ ggplot(data = imba_anno_merged_score_format_l1_baseline, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_baseline_annotation_f1_scores_celltype_ds.pdf" + "03_pbmc_ds_ablate_l1_baseline_annotation_f1_scores_celltype_ds.pdf" ), width = 16, height = 7, @@ -1899,7 +1899,7 @@ ggplot(data = imba_anno_merged_score_format_l2_baseline, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_baseline_annotation_f1_scores_celltype_ds.pdf" + "03_pbmc_ds_ablate_l2_baseline_annotation_f1_scores_celltype_ds.pdf" ), width = 16, height = 7, @@ -2139,7 +2139,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_allmethod_cluster_number_no_liger.pdf", + "outs/control/figures/03_pbmc_ds_ablate_allmethod_cluster_number_no_liger.pdf", width = 14, height = 8, device = cairo_pdf @@ -2177,7 +2177,7 @@ ggscatter(imba_clus_merged, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_clus_num_celltype_ari_corr_no_liger.pdf", + "outs/control/figures/03_pbmc_ds_ablate_clus_num_celltype_ari_corr_no_liger.pdf", width = 14, height = 8, device = cairo_pdf @@ -2212,7 +2212,7 @@ ggscatter(imba_clus_merged, theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 14)) ggsave( - "outs/control/figures/07_pbmc_ds_ablate_clus_num_batch_ari_corr_no_liger.pdf", + "outs/control/figures/03_pbmc_ds_ablate_clus_num_batch_ari_corr_no_liger.pdf", width = 14, height = 8, device = cairo_pdf @@ -2296,7 +2296,7 @@ ggplot(data = imba_dge_merged, aes( theme(legend.position = "None") ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "marker_gene_max_ranks_no_liger.pdf" ), width = 14, @@ -2351,7 +2351,7 @@ ggplot(data = imba_dge_merged, aes( theme(legend.position = "None") ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "marker_gene_max_ranks_per_method_no_liger.pdf" ), width = 14, @@ -2406,7 +2406,7 @@ lapply(methods, function(x) { dge_method_plt(imba_dge_merged, x) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", x, "_dge_rankings_no_liger.pdf" ), @@ -2578,7 +2578,7 @@ ht4 <- Heatmap( # Plot and save all of the heatmaps together marker_pert_hm <- ht1 + ht2 + ht3 + ht4 CairoPDF( - "outs/control/figures/07_marker_gene_pert_pbmc_control_heatmap_no_liger.pdf", + "outs/control/figures/03_marker_gene_pert_pbmc_control_heatmap_no_liger.pdf", width = 14, height = 6 ) @@ -2642,7 +2642,7 @@ ht3 <- Heatmap( ) marker_per_hm_no_celltype <- ht1 + ht2 + ht3 CairoPDF( - "outs/control/figures/07_marker_gene_pert_pbmc_control_heatmap_no_ctype_no_liger.pdf", + "outs/control/figures/03_marker_gene_pert_pbmc_control_heatmap_no_ctype_no_liger.pdf", width = 14, height = 6 ) @@ -2700,7 +2700,7 @@ ggplot(imba_dge_merged_top_10_var_genes, aes(x = Gene, y = `Max rank`)) + theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_dge_rankings_top_10_var_genes_no_liger.pdf" + "outs/control/figures/03_pbmc_ds_ablate_dge_rankings_top_10_var_genes_no_liger.pdf" ), width = 14, height = 8, @@ -2769,7 +2769,7 @@ lapply(methods, function(x) { dge_stdev_method_plt(gene_rank_variance_grouped, x) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", x, "_dge_rankings_method_type_stdev_no_liger.pdf" ), @@ -2828,7 +2828,7 @@ ggplot( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_dge_rankings_method_type_stdev_top_10_no_liger.pdf" ), width = 14, @@ -2891,7 +2891,7 @@ ggplot( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_dge_rankings_type_stdev_no_liger.pdf" ), width = 14, @@ -2961,7 +2961,7 @@ top_10_var_marker_genes_sankey <- sankeyNetwork( saveNetwork( top_10_var_marker_genes_sankey, file = paste0( - "outs/control/figures/07_pbmc_ds_ablate_", + "outs/control/figures/03_pbmc_ds_ablate_", "_top_var_dges_with_assoc_celltypes_no_liger.html" ), selfcontained = TRUE @@ -3104,7 +3104,7 @@ ggplot( ) ggsave( paste0( - "outs/control/figures/07_pbmc_ds_only_", + "outs/control/figures/03_pbmc_ds_only_", "_dge_rankings_celltype_marker_celltype_ds_compare_no_liger.pdf" ), width = 14, @@ -3165,7 +3165,7 @@ ggplot( ) ggsave( paste0( - "outs/control/figures/07_pbmc_ablated_only_", + "outs/control/figures/03_pbmc_ablated_only_", "_dge_rankings_celltype_marker_celltype_ablated_compare_no_liger.pdf" ), width = 14, @@ -3326,7 +3326,7 @@ ggplot(data = imba_anno_merged_score_format_l1, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_ds_no_liger.pdf" + "03_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_ds_no_liger.pdf" ), width = 16, height = 7, @@ -3377,7 +3377,7 @@ ggplot(data = imba_anno_merged_score_format_l2, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_ds_no_liger.pdf" + "03_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_ds_no_liger.pdf" ), width = 16, height = 7, @@ -3434,7 +3434,7 @@ ggplot(data = imba_anno_merged_score_format_l1_sd, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_sdev_no_liger.pdf" + "03_pbmc_ds_ablate_l1_annotation_f1_scores_celltype_sdev_no_liger.pdf" ), width = 7, height = 5, @@ -3478,7 +3478,7 @@ ggplot(data = imba_anno_merged_score_format_l2_sd, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_sdev_no_liger.pdf" + "03_pbmc_ds_ablate_l2_annotation_f1_scores_celltype_sdev_no_liger.pdf" ), width = 7, height = 5, @@ -3576,7 +3576,7 @@ ggplot(data = imba_anno_merged_all_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_t_cell_preds_barplot_no_liger.pdf" + "03_pbmc_ds_ablate_l1_annotation_t_cell_preds_barplot_no_liger.pdf" ), width = 10, height = 7, @@ -3612,7 +3612,7 @@ ggplot(data = imba_anno_merged_all_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_t_cell_preds_barplot_no_liger.pdf" + "03_pbmc_ds_ablate_l2_annotation_t_cell_preds_barplot_no_liger.pdf" ), width = 10, height = 7, @@ -3656,7 +3656,7 @@ ggplot(data = imba_anno_merged_all_cd4_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_cd4t_cell_preds", + "03_pbmc_ds_ablate_l1_annotation_cd4t_cell_preds", "_celltype_ds_specific_barplots_no_liger.pdf" ), width = 12, @@ -3689,7 +3689,7 @@ ggplot(data = imba_anno_merged_all_cd4_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_cd4t_cell_preds", + "03_pbmc_ds_ablate_l2_annotation_cd4t_cell_preds", "_celltype_ds_specific_barplots_no_liger.pdf" ), width = 12, @@ -3722,7 +3722,7 @@ ggplot(data = imba_anno_merged_all_cd8_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_annotation_cd8t_cell_preds", + "03_pbmc_ds_ablate_l1_annotation_cd8t_cell_preds", "_celltype_ds_specific_barplots_no_liger.pdf" ), width = 12, @@ -3755,7 +3755,7 @@ ggplot(data = imba_anno_merged_all_cd8_tcell, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_annotation_cd8t_cell_preds", + "03_pbmc_ds_ablate_l2_annotation_cd8t_cell_preds", "_celltype_ds_specific_barplots_no_liger.pdf" ), width = 12, @@ -3808,7 +3808,7 @@ ggplot(data = imba_anno_merged_score_format_l1_baseline, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l1_baseline_annotation_f1_scores_celltype_ds_no_liger.pdf" + "03_pbmc_ds_ablate_l1_baseline_annotation_f1_scores_celltype_ds_no_liger.pdf" ), width = 16, height = 7, @@ -3850,7 +3850,7 @@ ggplot(data = imba_anno_merged_score_format_l2_baseline, aes( ggsave( paste0( "outs/control/figures/", - "07_pbmc_ds_ablate_l2_baseline_annotation_f1_scores_celltype_ds_no_liger.pdf" + "03_pbmc_ds_ablate_l2_baseline_annotation_f1_scores_celltype_ds_no_liger.pdf" ), width = 16, height = 7, @@ -4037,7 +4037,7 @@ ggplot(test_concat, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/control/figures/07_t_cell_marker_perturbation_supp_analysis.pdf", + "outs/control/figures/03_t_cell_marker_perturbation_supp_analysis.pdf", width = 12, height = 6, device = cairo_pdf diff --git a/workflow/analysis/R/08_Iniq_Control_Fig_3_Analysis_Stat_Tests.R b/workflow/analysis/R/04_Iniq_Control_Fig_3_Analysis_Stat_Tests.R similarity index 98% rename from workflow/analysis/R/08_Iniq_Control_Fig_3_Analysis_Stat_Tests.R rename to workflow/analysis/R/04_Iniq_Control_Fig_3_Analysis_Stat_Tests.R index c817a53..59f139a 100644 --- a/workflow/analysis/R/08_Iniq_Control_Fig_3_Analysis_Stat_Tests.R +++ b/workflow/analysis/R/04_Iniq_Control_Fig_3_Analysis_Stat_Tests.R @@ -195,7 +195,7 @@ fwrite( clus_anova_result_dt, paste0( "outs/control/results/", - "08_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds.tsv" + "04_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds.tsv" ), sep = "\t", quote = FALSE, @@ -296,7 +296,7 @@ fwrite( dge_anova_result_dt, paste0( "outs/control/results/", - "08_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds.tsv" + "04_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds.tsv" ), sep = "\t", quote = FALSE, @@ -363,7 +363,7 @@ fwrite( marker_aov_results_concat, paste0( "outs/control/results/", - "08_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds.tsv" + "04_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds.tsv" ), sep = "\t", quote = FALSE, @@ -476,7 +476,7 @@ fwrite( marker_lm_summaries_concat, paste0( "outs/control/results/", - "08_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks.tsv" + "04_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks.tsv" ), sep = "\t", quote = FALSE, @@ -556,7 +556,7 @@ fwrite( multinomial_results_concat, paste0( "outs/control/results/", - "08_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", + "04_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", "coeff_multinom_tests.tsv" ), sep = "\t", @@ -777,7 +777,7 @@ fwrite( clus_anova_result_dt, paste0( "outs/control/results/", - "08_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds_no_liger.tsv" + "04_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -878,7 +878,7 @@ fwrite( dge_anova_result_dt, paste0( "outs/control/results/", - "08_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds_no_liger.tsv" + "04_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -945,7 +945,7 @@ fwrite( marker_aov_results_concat, paste0( "outs/control/results/", - "08_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds_no_liger.tsv" + "04_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -1058,7 +1058,7 @@ fwrite( marker_lm_summaries_concat, paste0( "outs/control/results/", - "08_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks_no_liger.tsv" + "04_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -1138,7 +1138,7 @@ fwrite( multinomial_results_concat, paste0( "outs/control/results/", - "08_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", + "04_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", "coeff_multinom_tests_no_liger.tsv" ), sep = "\t", diff --git a/workflow/analysis/R/09_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R b/workflow/analysis/R/05_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R similarity index 98% rename from workflow/analysis/R/09_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R rename to workflow/analysis/R/05_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R index e54a7da..aa4caee 100644 --- a/workflow/analysis/R/09_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R +++ b/workflow/analysis/R/05_Iniq_Control_Fig_3_Analysis_Stats_Multinomial_Low_Rep.R @@ -210,7 +210,7 @@ fwrite( clus_anova_result_dt, paste0( "outs/control/results/", - "09_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds_no_liger.tsv" + "05_pbmc_base_clus_num_leiden_aov_results_ctrl_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -311,7 +311,7 @@ fwrite( dge_anova_result_dt, paste0( "outs/control/results/", - "09_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds_no_liger.tsv" + "05_pbmc_base_dge_rank_aov_results_ctrl_gene_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -378,7 +378,7 @@ fwrite( marker_aov_results_concat, paste0( "outs/control/results/", - "09_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds_no_liger.tsv" + "05_pbmc_base_dge_specific_rank_aov_results_ctrl_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -491,7 +491,7 @@ fwrite( marker_lm_summaries_concat, paste0( "outs/control/results/", - "09_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks_no_liger.tsv" + "05_pbmc_base_dge_rank_coeffs_celltype_ds_method_importance_ranks_no_liger.tsv" ), sep = "\t", quote = FALSE, @@ -571,7 +571,7 @@ fwrite( multinomial_results_concat, paste0( "outs/control/results/", - "09_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", + "05_pbmc_base_ds_dge_marker_celltypes_top_ds_celltype_", "coeff_multinom_tests_low_rep_no_liger.tsv" ), sep = "\t", diff --git a/workflow/analysis/R/10_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R b/workflow/analysis/R/06_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R similarity index 97% rename from workflow/analysis/R/10_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R rename to workflow/analysis/R/06_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R index 256ae1e..8d1d154 100644 --- a/workflow/analysis/R/10_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R +++ b/workflow/analysis/R/06_Iniq_Real_Datasets_Fig_4_Analysis_Plots.R @@ -279,7 +279,7 @@ ggplot( ggsave( paste0( "outs/lowcap_modified/figures/", - "10_pbmc_full_dataset_vs_control_dataset_celltype_ari_no_ds.pdf" + "06_pbmc_full_dataset_vs_control_dataset_celltype_ari_no_ds.pdf" ), width = 9, height = 6, @@ -319,7 +319,7 @@ ggplot( ggsave( paste0( "outs/lowcap_modified/figures/", - "10_pbmc_full_dataset_vs_control_dataset_batch_ari_no_ds.pdf" + "06_pbmc_full_dataset_vs_control_dataset_batch_ari_no_ds.pdf" ), width = 9, height = 6, @@ -369,7 +369,7 @@ ggplot( y = "Celltype 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_2_batch_bal_celltype_relatedness.pdf", + "outs/lowcap_modified/figures/06_pbmc_2_batch_bal_celltype_relatedness.pdf", width = 7, height = 7, device = cairo_pdf @@ -416,7 +416,7 @@ ggplot( y = "Celltype 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_2_batch_imba_celltype_relatedness.pdf", + "outs/lowcap_modified/figures/06_pbmc_2_batch_imba_celltype_relatedness.pdf", width = 7, height = 7, device = cairo_pdf @@ -552,7 +552,7 @@ knn_relatedness_plot <- function( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", dataset, "_knn_results_celltype_relatedness_comp.pdf" ), @@ -633,7 +633,7 @@ knn_support_plot <- function(dataset, knn_class_df, plot_height, plot_width) { theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", dataset, "_knn_results_celltype_num_comp.pdf" ), @@ -694,7 +694,7 @@ ggplot( geom_point(aes(color = `F1-score`)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", "min_pca_dist_support_plotting_test.pdf" ), width = 12, @@ -710,7 +710,7 @@ ggplot( geom_point(aes(color = `Min PCA cosine dist`)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", "min_pca_dist_support_plotting_test_2.pdf" ), width = 12, @@ -766,7 +766,7 @@ ggplot( y = "Celltype 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_4_batch_bal_celltype_relatedness.pdf", + "outs/lowcap_modified/figures/06_pbmc_4_batch_bal_celltype_relatedness.pdf", width = 7, height = 7, device = cairo_pdf @@ -1063,7 +1063,7 @@ ggplot( ggsave( paste0( "outs/lowcap_modified/figures/", - "10_pbmc_full_dataset_vs_control_dataset_celltype_ari_no_ds_no_liger.pdf" + "06_pbmc_full_dataset_vs_control_dataset_celltype_ari_no_ds_no_liger.pdf" ), width = 9, height = 6, @@ -1103,7 +1103,7 @@ ggplot( ggsave( paste0( "outs/lowcap_modified/figures/", - "10_pbmc_full_dataset_vs_control_dataset_batch_ari_no_ds_no_liger.pdf" + "06_pbmc_full_dataset_vs_control_dataset_batch_ari_no_ds_no_liger.pdf" ), width = 9, height = 6, @@ -1187,7 +1187,7 @@ ggplot( y = "Cell-type 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_2_batch_bal_celltype_relatedness_no_liger.pdf", + "outs/lowcap_modified/figures/06_pbmc_2_batch_bal_celltype_relatedness_no_liger.pdf", width = 7, height = 7, device = cairo_pdf @@ -1234,7 +1234,7 @@ ggplot( y = "Cell-type 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_2_batch_imba_celltype_relatedness_no_liger.pdf", + "outs/lowcap_modified/figures/06_pbmc_2_batch_imba_celltype_relatedness_no_liger.pdf", width = 7, height = 7, device = cairo_pdf @@ -1418,7 +1418,7 @@ knn_relatedness_plot <- function( theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", dataset, "_knn_results_celltype_relatedness_comp_no_liger.pdf" ), @@ -1499,7 +1499,7 @@ knn_support_plot <- function(dataset, knn_class_df, plot_height, plot_width) { theme(legend.text = element_text(size = 14)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", dataset, "_knn_results_celltype_num_comp_no_liger.pdf" ), @@ -1560,7 +1560,7 @@ ggplot( geom_point(aes(color = `F1-score`)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", "min_pca_dist_support_plotting_test_no_liger.pdf" ), width = 12, @@ -1576,7 +1576,7 @@ ggplot( geom_point(aes(color = `Min PCA cosine dist`)) ggsave( paste0( - "outs/lowcap_modified/figures/10_", + "outs/lowcap_modified/figures/06_", "min_pca_dist_support_plotting_test_2_no_liger.pdf" ), width = 12, @@ -1633,7 +1633,7 @@ ggplot( y = "Cell-type 2" ) ggsave( - "outs/lowcap_modified/figures/10_pbmc_4_batch_bal_celltype_relatedness_no_liger.pdf", + "outs/lowcap_modified/figures/06_pbmc_4_batch_bal_celltype_relatedness_no_liger.pdf", width = 7, height = 7, device = cairo_pdf @@ -1685,7 +1685,7 @@ ggplot( y = "Cell-type 2" ) ggsave( - "outs/lowcap_modified/figures/10_mouse_hindbrain_6_batch_celltype_relatedness_no_liger.pdf", + "outs/lowcap_modified/figures/06_mouse_hindbrain_6_batch_celltype_relatedness_no_liger.pdf", width = 14, height = 14, device = cairo_pdf @@ -1737,7 +1737,7 @@ ggplot( y = "Cell-type 2" ) ggsave( - "outs/lowcap_modified/figures/10_pdac_8_batch_celltype_relatedness_no_liger.pdf", + "outs/lowcap_modified/figures/06_pdac_8_batch_celltype_relatedness_no_liger.pdf", width = 8, height = 8, device = cairo_pdf diff --git a/workflow/analysis/R/10B_Iniq_Real_Datasets_Fig_4_Stat_Tests.R b/workflow/analysis/R/07_Iniq_Real_Datasets_Fig_4_Stat_Tests.R similarity index 98% rename from workflow/analysis/R/10B_Iniq_Real_Datasets_Fig_4_Stat_Tests.R rename to workflow/analysis/R/07_Iniq_Real_Datasets_Fig_4_Stat_Tests.R index bb44f54..2458854 100644 --- a/workflow/analysis/R/10B_Iniq_Real_Datasets_Fig_4_Stat_Tests.R +++ b/workflow/analysis/R/07_Iniq_Real_Datasets_Fig_4_Stat_Tests.R @@ -291,7 +291,7 @@ anova_result_dt_batch_celltype_ari_pbmc_2$q_val <- p.adjust( # Save the results fwrite( anova_result_dt_batch_celltype_ari_pbmc_2, - "outs/lowcap_modified/results/10B_pbmc_2_bal_imbal_c_b_ari_anova_tests.tsv", + "outs/lowcap_modified/results/07_pbmc_2_bal_imbal_c_b_ari_anova_tests.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -418,7 +418,7 @@ relatedness_anova_results <- mapply( relatedness_anova_results_concat <- Reduce(rbind, relatedness_anova_results) fwrite( relatedness_anova_results_concat, - "outs/lowcap_modified/results/10B_all_ds_anova_relatedness_results.tsv", + "outs/lowcap_modified/results/07_all_ds_anova_relatedness_results.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -479,7 +479,7 @@ support_anova_results <- mapply( support_anova_results_concat <- Reduce(rbind, support_anova_results) fwrite( support_anova_results_concat, - "outs/lowcap_modified/results/10B_all_ds_anova_support_results.tsv", + "outs/lowcap_modified/results/07_all_ds_anova_support_results.tsv", sep = "\t", quote = FALSE, row.names = FALSE, diff --git a/workflow/analysis/R/12_Fig_6_PDAC_Analysis_Plots.R b/workflow/analysis/R/08_Fig_6_PDAC_Analysis_Plots.R similarity index 97% rename from workflow/analysis/R/12_Fig_6_PDAC_Analysis_Plots.R rename to workflow/analysis/R/08_Fig_6_PDAC_Analysis_Plots.R index db47504..35a95a7 100644 --- a/workflow/analysis/R/12_Fig_6_PDAC_Analysis_Plots.R +++ b/workflow/analysis/R/08_Fig_6_PDAC_Analysis_Plots.R @@ -165,7 +165,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_ds_ablate_methods_nclusters.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_ds_ablate_methods_nclusters.pdf", width = 12, height = 7, device = cairo_pdf @@ -288,7 +288,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp/figures/12_celltype_ari_ds_effects_heatmap.pdf", + "outs/pdac_comp/figures/08_celltype_ari_ds_effects_heatmap.pdf", width = 8, height = 4 ) @@ -393,7 +393,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp/figures/12_batch_ari_ds_effects_heatmap.pdf", + "outs/pdac_comp/figures/08_batch_ari_ds_effects_heatmap.pdf", width = 8, height = 4 ) @@ -477,7 +477,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_ds_ablate_methods_knn_f1_score.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_ds_ablate_methods_knn_f1_score.pdf", width = 16, height = 7, device = cairo_pdf @@ -572,7 +572,7 @@ ggplot( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_batches_celltype_n_cells.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_batches_celltype_n_cells.pdf", width = 7, height = 5, device = cairo_pdf @@ -741,7 +741,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_ds_ablate_methods_nclusters_no_liger.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_ds_ablate_methods_nclusters_no_liger.pdf", width = 12, height = 7, device = cairo_pdf @@ -864,7 +864,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp/figures/12_celltype_ari_ds_effects_heatmap_no_liger.pdf", + "outs/pdac_comp/figures/08_celltype_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 4 ) @@ -969,7 +969,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp/figures/12_batch_ari_ds_effects_heatmap_no_liger.pdf", + "outs/pdac_comp/figures/08_batch_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 4 ) @@ -1069,7 +1069,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp/figures/12_celltype_balanced_ari_ds_effects_heatmap_no_liger.pdf", + "outs/pdac_comp/figures/08_celltype_balanced_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 4 ) @@ -1153,7 +1153,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_ds_ablate_methods_knn_f1_score_no_liger.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_ds_ablate_methods_knn_f1_score_no_liger.pdf", width = 16, height = 7, device = cairo_pdf @@ -1215,7 +1215,7 @@ ggplot(data = imba_knn_merged, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_non_compart_specific_ds_ablate_methods_knn_f1_score_no_liger.pdf", + "outs/pdac_comp/figures/08_pdac_non_compart_specific_ds_ablate_methods_knn_f1_score_no_liger.pdf", width = 24, height = 12, device = cairo_pdf @@ -1310,7 +1310,7 @@ ggplot( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp/figures/12_pdac_compartment_batches_celltype_n_cells_no_liger.pdf", + "outs/pdac_comp/figures/08_pdac_compartment_batches_celltype_n_cells_no_liger.pdf", width = 7, height = 5, device = cairo_pdf diff --git a/workflow/analysis/R/12B_Iniq_PDAC_Fig_6_Stat_Tests.R b/workflow/analysis/R/09_Iniq_PDAC_Fig_6_Stat_Tests.R similarity index 98% rename from workflow/analysis/R/12B_Iniq_PDAC_Fig_6_Stat_Tests.R rename to workflow/analysis/R/09_Iniq_PDAC_Fig_6_Stat_Tests.R index 8a1721d..20d4c01 100644 --- a/workflow/analysis/R/12B_Iniq_PDAC_Fig_6_Stat_Tests.R +++ b/workflow/analysis/R/09_Iniq_PDAC_Fig_6_Stat_Tests.R @@ -207,7 +207,7 @@ knn_anova_comp_results knn_anova_comp_results_concat <- Reduce(rbind, knn_anova_comp_results) fwrite( knn_anova_comp_results_concat, - "outs/pdac_comp/results/12B_comp_specific_ds_knn_f1_score_anovas.tsv", + "outs/pdac_comp/results/09_comp_specific_ds_knn_f1_score_anovas.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -270,7 +270,7 @@ ggplot(data = knn_aov_comp_df_melted, aes(Covariates, value)) + ggsave( paste0( "outs/pdac_comp/figures/", - "12B_pdac_knn_aov_comp_ds_f_statistic.pdf" + "09_pdac_knn_aov_comp_ds_f_statistic.pdf" ), width = 12, height = 12, diff --git a/workflow/analysis/R/13_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R b/workflow/analysis/R/10_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R similarity index 94% rename from workflow/analysis/R/13_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R rename to workflow/analysis/R/10_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R index 0093ccb..39d3922 100644 --- a/workflow/analysis/R/13_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R +++ b/workflow/analysis/R/10_Iniq_Balanced_Metrics_Results_Fig_7_Analysis_Plots.R @@ -118,7 +118,7 @@ p_7a_1 <- ggplot(data = bal_7A_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7a_1 ggsave( - "outs/balanced_metrics/figures/13_7A_trial_class_coordinates.pdf", + "outs/balanced_metrics/figures/10_7A_trial_class_coordinates.pdf", width = 6, height = 6 ) @@ -146,7 +146,7 @@ p_7a_2 <- ggplot(data = bal_7A_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7a_2 ggsave( - "outs/balanced_metrics/figures/13_7A_trial_cluster_coordinates.pdf", + "outs/balanced_metrics/figures/10_7A_trial_cluster_coordinates.pdf", width = 6, height = 6 ) @@ -199,7 +199,7 @@ p_7a_3 <- ggplot( coord_flip() p_7a_3 ggsave( - "outs/balanced_metrics/figures/13_7A_metrics_barplot.pdf", + "outs/balanced_metrics/figures/10_7A_metrics_barplot.pdf", width = 8, height = 8, device = cairo_pdf @@ -216,7 +216,7 @@ all_7a_plots <- plot_grid( ncol = 1 ) save_plot( - "outs/balanced_metrics/figures/13_7A_all_plots.pdf", + "outs/balanced_metrics/figures/10_7A_all_plots.pdf", all_7a_plots, base_asp = 1, base_height = 8, @@ -248,7 +248,7 @@ p_7b_1 <- ggplot(data = bal_7B_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7b_1 ggsave( - "outs/balanced_metrics/figures/13_7B_trial_class_coordinates.pdf", + "outs/balanced_metrics/figures/10_7B_trial_class_coordinates.pdf", width = 6, height = 6 ) @@ -276,7 +276,7 @@ p_7b_2 <- ggplot(data = bal_7B_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7b_2 ggsave( - "outs/balanced_metrics/figures/13_7B_trial_cluster_coordinates.pdf", + "outs/balanced_metrics/figures/10_7B_trial_cluster_coordinates.pdf", width = 6, height = 6 ) @@ -329,7 +329,7 @@ p_7b_3 <- ggplot( scale_y_continuous(breaks = scales::pretty_breaks(n = 3), limits = c(0, 1)) p_7b_3 ggsave( - "outs/balanced_metrics/figures/13_7B_metrics_barplot.pdf", + "outs/balanced_metrics/figures/10_7B_metrics_barplot.pdf", width = 8, height = 8, device = cairo_pdf @@ -346,7 +346,7 @@ all_7b_plots <- plot_grid( ncol = 1 ) save_plot( - "outs/balanced_metrics/figures/13_7B_all_plots.pdf", + "outs/balanced_metrics/figures/10_7B_all_plots.pdf", all_7b_plots, base_asp = 1, base_height = 8, @@ -379,7 +379,7 @@ ggplot(data = bal_7C_cluster_df, aes(x = x, y = y)) + theme(aspect.ratio = 1) + guides(colour = guide_legend(override.aes = list(size=3))) ggsave( - "outs/balanced_metrics/figures/13_7C_trial_celltype_coordinates.pdf", + "outs/balanced_metrics/figures/10_7C_trial_celltype_coordinates.pdf", width = 7, height = 7 ) @@ -406,7 +406,7 @@ ggplot(data = bal_7C_cluster_df, aes(x = x, y = y)) + theme(aspect.ratio = 1) + guides(colour = guide_legend(override.aes = list(size=3))) ggsave( - "outs/balanced_metrics/figures/13_7C_trial_cluster_coordinates.pdf", + "outs/balanced_metrics/figures/10_7C_trial_cluster_coordinates.pdf", width = 7, height = 7 ) @@ -460,7 +460,7 @@ ggplot( theme(legend.text = element_text(size = 16)) + theme(aspect.ratio = 1) ggsave( - "outs/balanced_metrics/figures/13_7C_metrics_barplot.pdf", + "outs/balanced_metrics/figures/10_7C_metrics_barplot.pdf", width = 6, height = 6, device = cairo_pdf @@ -490,7 +490,7 @@ p_7d_1 <- ggplot(data = bal_7D_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7d_1 ggsave( - "outs/balanced_metrics/figures/13_7D_trial_celltype_coordinates.pdf", + "outs/balanced_metrics/figures/10_7D_trial_celltype_coordinates.pdf", width = 7, height = 7 ) @@ -517,7 +517,7 @@ p_7d_2 <- ggplot(data = bal_7D_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7d_2 ggsave( - "outs/balanced_metrics/figures/13_7D_trial_batch_coordinates.pdf", + "outs/balanced_metrics/figures/10_7D_trial_batch_coordinates.pdf", width = 7, height = 7 ) @@ -545,7 +545,7 @@ p_7d_3 <- ggplot(data = bal_7D_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7d_3 ggsave( - "outs/balanced_metrics/figures/13_7D_trial_cluster_coordinates.pdf", + "outs/balanced_metrics/figures/10_7D_trial_cluster_coordinates.pdf", width = 7, height = 7 ) @@ -603,7 +603,7 @@ p_7d_4 <- ggplot( p_7d_4 ggsave( - "outs/balanced_metrics/figures/13_7D_metrics_barplot.pdf", + "outs/balanced_metrics/figures/10_7D_metrics_barplot.pdf", width = 6, height = 6, device = cairo_pdf @@ -621,7 +621,7 @@ all_7d_plots <- plot_grid( ncol = 4 ) save_plot( - "outs/balanced_metrics/figures/13_7D_all_plots.pdf", + "outs/balanced_metrics/figures/10_7D_all_plots.pdf", all_7d_plots, base_asp = 1, base_height = 4, @@ -653,7 +653,7 @@ p_7e_1 <- ggplot(data = bal_7E_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7e_1 ggsave( - "outs/balanced_metrics/figures/13_7E_trial_celltype_coordinates_facet.pdf", + "outs/balanced_metrics/figures/10_7E_trial_celltype_coordinates_facet.pdf", width = 10, height = 8 ) @@ -681,7 +681,7 @@ p_7e_2 <- ggplot(data = bal_7E_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7e_2 ggsave( - "outs/balanced_metrics/figures/13_7e_trial_batch_coordinates_facet.pdf", + "outs/balanced_metrics/figures/10_7e_trial_batch_coordinates_facet.pdf", width = 10, height = 8 ) @@ -745,7 +745,7 @@ p_7e_3 <- ggplot(data = bal_7E_cluster_df, aes(x = x, y = y)) + guides(colour = guide_legend(override.aes = list(size=3))) p_7e_3 ggsave( - "outs/balanced_metrics/figures/13_7E_trial_cluster_coordinates.pdf", + "outs/balanced_metrics/figures/10_7E_trial_cluster_coordinates.pdf", width = 10, height = 8 ) @@ -820,7 +820,7 @@ p_7e_4 <- ggplot( coord_flip() p_7e_4 ggsave( - "outs/balanced_metrics/figures/13_7E_trial_avg_metric_score_imbal.pdf", + "outs/balanced_metrics/figures/10_7E_trial_avg_metric_score_imbal.pdf", width = 7, height = 7 ) @@ -863,7 +863,7 @@ p_7e_5 <- ggplot( coord_flip() p_7e_5 ggsave( - "outs/balanced_metrics/figures/13_7E_trial_avg_metric_score_bal.pdf", + "outs/balanced_metrics/figures/10_7E_trial_avg_metric_score_bal.pdf", width = 7, height = 7 ) @@ -883,7 +883,7 @@ p_7e_all <- plot_grid( ) p_7e_all save_plot( - "outs/balanced_metrics/figures/13_7E_all_plots.pdf", + "outs/balanced_metrics/figures/10_7E_all_plots.pdf", p_7e_all, base_asp = 1, base_height = 18, @@ -923,7 +923,7 @@ ggplot(data = bal_7E_metrics_df_sub, aes(x = Metric, y = Value)) + theme(axis.text.y = element_text(size = 16)) + coord_flip() ggsave( - "outs/balanced_metrics/figures/13_7E_trial_bal_imbal_ari_ami_scores.pdf", + "outs/balanced_metrics/figures/10_7E_trial_bal_imbal_ari_ami_scores.pdf", width = 16, height = 7 ) diff --git a/workflow/analysis/R/19_Supplementary_TI_Analysis.R b/workflow/analysis/R/11_Fig_4_TI_Analysis.R similarity index 96% rename from workflow/analysis/R/19_Supplementary_TI_Analysis.R rename to workflow/analysis/R/11_Fig_4_TI_Analysis.R index 21c5ec9..77f579e 100644 --- a/workflow/analysis/R/19_Supplementary_TI_Analysis.R +++ b/workflow/analysis/R/11_Fig_4_TI_Analysis.R @@ -129,7 +129,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_pearson_corr_ds_celltype_method.pdf" + "11_chondrocyte_ti_pearson_corr_ds_celltype_method.pdf" ), width = 14, height = 8, @@ -184,7 +184,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_spearman_corr_ds_celltype_method.pdf" + "11_chondrocyte_ti_spearman_corr_ds_celltype_method.pdf" ), width = 14, height = 8, @@ -239,7 +239,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_kendall_corr_ds_celltype_method.pdf" + "11_chondrocyte_ti_kendall_corr_ds_celltype_method.pdf" ), width = 14, height = 8, @@ -379,7 +379,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_pearson_corr_ds_celltype_method_no_liger.pdf" + "11_chondrocyte_ti_pearson_corr_ds_celltype_method_no_liger.pdf" ), width = 14, height = 8, @@ -443,7 +443,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_spearman_corr_ds_celltype_method_no_liger.pdf" + "11_chondrocyte_ti_spearman_corr_ds_celltype_method_no_liger.pdf" ), width = 28, height = 8, @@ -507,7 +507,7 @@ ggplot( ggsave( paste0( "outs/control_ti_only/figures/", - "19_chondrocyte_ti_kendall_corr_ds_celltype_method_no_liger.pdf" + "11_chondrocyte_ti_kendall_corr_ds_celltype_method_no_liger.pdf" ), width = 14, height = 8, @@ -597,7 +597,7 @@ DimPlot(dev_combined, reduction = "umap", group.by = "celltype") + scale_color_brewer(palette = "Dark2") + theme(aspect.ratio = 1) ggsave( - "outs/control_ti_only/figures/19_dev_balanced_combined_celltypes.pdf", + "outs/control_ti_only/figures/11_dev_balanced_combined_celltypes.pdf", width = 6, height = 6 ) @@ -610,7 +610,7 @@ DimPlot(dev_combined, reduction = "umap", group.by = "batch") + scale_color_brewer(palette = "Set1") + theme(aspect.ratio = 1) ggsave( - "outs/control_ti_only/figures/19_dev_balanced_combined_batch.pdf", + "outs/control_ti_only/figures/11_dev_balanced_combined_batch.pdf", width = 6, height = 6 ) @@ -681,7 +681,7 @@ fwrite( ti_anova_result_dt, paste0( "outs/control_ti_only/results/", - "19_cao_et_al_ti_leiden_spearman_corr_aov_results_ctrl_method_celltype_ds_no_liger.tsv" + "11_cao_et_al_ti_leiden_spearman_corr_aov_results_ctrl_method_celltype_ds_no_liger.tsv" ), sep = "\t", quote = FALSE, diff --git a/workflow/analysis/R/20_Fig_6_PDAC_Reanno_Analysis_Plots.R b/workflow/analysis/R/12_Fig_6_PDAC_Reanno_Analysis_Plots.R similarity index 97% rename from workflow/analysis/R/20_Fig_6_PDAC_Reanno_Analysis_Plots.R rename to workflow/analysis/R/12_Fig_6_PDAC_Reanno_Analysis_Plots.R index eee6e39..2f1ce59 100644 --- a/workflow/analysis/R/20_Fig_6_PDAC_Reanno_Analysis_Plots.R +++ b/workflow/analysis/R/12_Fig_6_PDAC_Reanno_Analysis_Plots.R @@ -145,7 +145,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_ds_ablate_methods_nclusters.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_ds_ablate_methods_nclusters.pdf", width = 12, height = 7, device = cairo_pdf @@ -268,7 +268,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp_reanno/figures/20_celltype_ari_ds_effects_heatmap.pdf", + "outs/pdac_comp_reanno/figures/12_celltype_ari_ds_effects_heatmap.pdf", width = 8, height = 4 ) @@ -373,7 +373,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp_reanno/figures/20_batch_ari_ds_effects_heatmap.pdf", + "outs/pdac_comp_reanno/figures/12_batch_ari_ds_effects_heatmap.pdf", width = 8, height = 4 ) @@ -457,7 +457,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_ds_ablate_methods_knn_f1_score.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_ds_ablate_methods_knn_f1_score.pdf", width = 16, height = 7, device = cairo_pdf @@ -552,7 +552,7 @@ ggplot( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_batches_celltype_n_cells.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_batches_celltype_n_cells.pdf", width = 7, height = 5, device = cairo_pdf @@ -698,7 +698,7 @@ ggplot(data = imba_clus_merged, aes( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_ds_ablate_methods_nclusters_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_ds_ablate_methods_nclusters_no_liger.pdf", width = 12, height = 7, device = cairo_pdf @@ -821,7 +821,7 @@ ht3 = Heatmap( ) celltype_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp_reanno/figures/20_celltype_ari_ds_effects_heatmap_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_celltype_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 4 ) @@ -926,7 +926,7 @@ ht3 = Heatmap( ) batch_ari_hm <- ht1 + ht2 + ht3 CairoPDF( - "outs/pdac_comp_reanno/figures/20_batch_ari_ds_effects_heatmap_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_batch_ari_ds_effects_heatmap_no_liger.pdf", width = 8, height = 4 ) @@ -1010,7 +1010,7 @@ ggplot(data = imba_knn_merged_celltype, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_ds_ablate_methods_knn_f1_score_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_ds_ablate_methods_knn_f1_score_no_liger.pdf", width = 16, height = 7, device = cairo_pdf @@ -1072,7 +1072,7 @@ ggplot(data = imba_knn_merged, aes(x = `Method`, y = `F1-score`)) + theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_non_compart_specific_ds_ablate_methods_knn_f1_score_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_non_compart_specific_ds_ablate_methods_knn_f1_score_no_liger.pdf", width = 24, height = 12, device = cairo_pdf @@ -1167,7 +1167,7 @@ ggplot( theme(legend.title = element_text(size = 16)) + theme(legend.text = element_text(size = 16)) ggsave( - "outs/pdac_comp_reanno/figures/20_pdac_comp_reannoartment_batches_celltype_n_cells_no_liger.pdf", + "outs/pdac_comp_reanno/figures/12_pdac_comp_reannoartment_batches_celltype_n_cells_no_liger.pdf", width = 7, height = 5, device = cairo_pdf diff --git a/workflow/analysis/R/21_Fig_6_PDAC_Reanno_Stats_Tests.R b/workflow/analysis/R/13_Fig_6_PDAC_Reanno_Stats_Tests.R similarity index 98% rename from workflow/analysis/R/21_Fig_6_PDAC_Reanno_Stats_Tests.R rename to workflow/analysis/R/13_Fig_6_PDAC_Reanno_Stats_Tests.R index e9ccfb8..1e2a384 100644 --- a/workflow/analysis/R/21_Fig_6_PDAC_Reanno_Stats_Tests.R +++ b/workflow/analysis/R/13_Fig_6_PDAC_Reanno_Stats_Tests.R @@ -184,7 +184,7 @@ knn_anova_comp_results knn_anova_comp_results_concat <- Reduce(rbind, knn_anova_comp_results) fwrite( knn_anova_comp_results_concat, - "outs/pdac_comp_reanno/results/21_comp_specific_ds_knn_f1_score_anovas.tsv", + "outs/pdac_comp_reanno/results/13_comp_specific_ds_knn_f1_score_anovas.tsv", sep = "\t", quote = FALSE, row.names = FALSE, @@ -247,7 +247,7 @@ ggplot(data = knn_aov_comp_df_melted, aes(Covariates, value)) + ggsave( paste0( "outs/pdac_comp_reanno/figures/", - "21_pdac_knn_aov_comp_ds_f_statistic.pdf" + "13_pdac_knn_aov_comp_ds_f_statistic.pdf" ), width = 12, height = 12, diff --git a/workflow/analysis/R/21_PBMC_perturbation_umap_plots.R b/workflow/analysis/R/14_PBMC_perturbation_umap_plots.R similarity index 98% rename from workflow/analysis/R/21_PBMC_perturbation_umap_plots.R rename to workflow/analysis/R/14_PBMC_perturbation_umap_plots.R index 15549dd..c17f9e3 100644 --- a/workflow/analysis/R/21_PBMC_perturbation_umap_plots.R +++ b/workflow/analysis/R/14_PBMC_perturbation_umap_plots.R @@ -72,7 +72,7 @@ if (!dir.exists("outs/umap/results")) { dir.create("outs/umap/results", recursive = TRUE) } if (!dir.exists("outs/umap/figures")) { - dir.create("outs/umap/figures") + dir.create("outs/umap/figures", recursive = TRUE) } # Create function to loop over the umap files and return the results